Chlamydia trachomatis is the most common sexually transmitted bacterial pathogen in the US with an estimated 5 million cases annually. Studies have been in progress to define the clinical spectrum of chlamydial infection, to develop improved diagnostic assays and to examine the pathogenesis of chlamydial infection. Studies of genital chlamydial infection in patients attending sexually transmitted diseases clinics have demonstrated a prevalence of 15% in men and women with and without symptoms. Prevalence varied little by either sex, symptoms, number of sex partners or the patient's relationship to his sex partners, although co-infection with N. gonorrhoea and C. trachomatis was quite frequent in this population. Utilization of polymerase chain reaction (PCR) nearly doubled the sensitivity of culture for the detection of C. trachomatis. Among sexual partnerships infection was identified by PCR in 75% of male partners of infected females compared to only 39% by culture. Sequence analysis of amplified chlamydia DNA from partners identified the same serovar and further supported the accuracy of this assay. In an evaluation of a new molecular assay called ligase chain reaction (LCR) we identified chlamydia infection in 17.8% of urine samples collected from 1,500 symptomatic and asymptomatic men compared to only 9% by urethral culture. Screening of urine samples with molecular amplification assays may provide a highly cost-effective, noninvasive method for widespread screening of chlamydia. We also developed a new serologic technique for the measurement of specific antibodies to major outer membrane protein MOMP by producing a radiolabeled protein following PCR amplification, DNA transcription, and translation of MOMP protein. This serologic assay was then utilized to demonstrate a serologic rise in specific anti-MOMP antibodies in MOMP-vaccinated primates, which directly correlated with decreased infectious load. Clinical studies utilizing primer sets from the 16s rRNA of C. pneumoniae have demonstrated a marked increase in sensitivity and specificity of PCR for detection of C. pneumoniae in clinical pneumonia. Utilizing this assay, C. pneumoniae was identified in approximately 8% of nearly 700 patients with respiratory disease and in none of asymptomatic individuals.